4nx1 - Revision history

OCA at 08:44, 18 January 2023

OCA — Wed, 18 Jan 2023 08:44:22 GMT

←Older revision		Revision as of 08:44, 18 January 2023
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	==Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate==		==Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate==
-	<StructureSection load='4nx1' size='340' side='right' caption='[[4nx1]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4nx1' size='340' side='right'caption='[[4nx1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nx1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sulfitobacter_sp.~~_nas~~-14.1 Sulfitobacter sp. ~~nas~~-14.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NX1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NX1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nx1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfitobacter_sp._NAS-14.1 Sulfitobacter sp. NAS-14.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NX1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NX1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=X1X:ALPHA-D-TALOPYRANURONIC+ACID'>X1X</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=X1X:ALPHA-D-TALOPYRANURONIC+ACID'>X1X</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [https://pdbe.org/4nx1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [https://www.ebi.ac.uk/pdbsum/4nx1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nx1 ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">NAS141_03721 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314267 Sulfitobacter sp. NAS-14.1])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [~~http~~://pdbe.org/4nx1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nx1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nx1 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCTP_SULSN DCTP_SULSN] Solute-binding protein that binds D-mannuronate and D-taluronate (in vitro) (PubMed:25540822). Probably part of a tripartite ATP-independent periplasmic (TRAP) transport system that mediates solute transport into the cytoplasm.<ref>PMID:25540822</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Sulfitobacter sp. ~~nas~~-14 1]]	+	[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Sulfitobacter sp. NAS-14 1]]
-	[[Category: ~~Attonito, J D~~]]	+	[[Category: Al Obaidi NF]]
-	[[Category: ~~Chowdhury, S~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~EFI, Enzyme Function Initiative~~]]	+	[[Category: Attonito JD]]
-	[[Category: Evans, B]]	+	[[Category: Chowdhury S]]
-	[[Category: Gerlt~~, J A]]~~	+	[[Category: Evans B]]
-	~~[[Category: Glenn, A Scott~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Hillerich, B]]	+	[[Category: Hillerich B]]
-	[[Category: Imker~~, H J~~]]	+	[[Category: Imker HJ]]
-	[[Category: Love, J]]	+	[[Category: Love J]]
-	[[Category: Morisco~~, L L~~]]	+	[[Category: Morisco LL]]
-	[[Category: ~~Obaidi, N F.Al~~]]	+	[[Category: Scott Glenn A]]
-	[[Category: Seidel~~, R D~~]]	+	[[Category: Seidel RD]]
-	[[Category: Sojitra, S]]	+	[[Category: Sojitra S]]
-	[[Category: Stead, M]]	+	[[Category: Stead M]]
-	[[Category: Vetting~~, M W~~]]	+	[[Category: Vetting MW]]
-	[[Category: Wasserman~~, S R]]~~	+	[[Category: Wasserman SR]]
-	~~[[Category: Efi]]~~	+
-	~~[[Category: Enzyme function initiative]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Trap periplasmic solute binding family~~]]	+

OCA at 16:54, 2 January 2017

OCA — Mon, 02 Jan 2017 16:54:29 GMT

←Older revision		Revision as of 16:54, 2 January 2017
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		+
	==Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate==		==Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate==
	<StructureSection load='4nx1' size='340' side='right' caption='[[4nx1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4nx1' size='340' side='right' caption='[[4nx1]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAS141_03721 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314267 Sulfitobacter sp. NAS-14.1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAS141_03721 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314267 Sulfitobacter sp. NAS-14.1])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [http://www.ebi.ac.uk/pdbsum/4nx1 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [http://pdbe.org/4nx1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [http://www.ebi.ac.uk/pdbsum/4nx1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nx1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4nx1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:53, 25 February 2015

OCA — Wed, 25 Feb 2015 07:53:34 GMT

←Older revision		Revision as of 07:53, 25 February 2015
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [http://www.ebi.ac.uk/pdbsum/4nx1 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [http://www.ebi.ac.uk/pdbsum/4nx1 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.
		+
		+	Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.,Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822<ref>PMID:25540822</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:55, 5 January 2015

OCA — Mon, 05 Jan 2015 08:55:32 GMT

←Older revision		Revision as of 08:55, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4nx1\| PDB=4nx1 \| SCENE= }}~~	+	==Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate==
-	===Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate===	+	<StructureSection load='4nx1' size='340' side='right' caption='[[4nx1]], [[Resolution\|resolution]] 1.60Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4nx1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfitobacter_sp._nas-14.1 Sulfitobacter sp. nas-14.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NX1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NX1 FirstGlance]. <br>
-	[[4nx1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NX1 OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=X1X:ALPHA-D-TALOPYRANURONIC+ACID'>X1X</scene></td></tr>
-	[[Category: Almo, S C.]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: Attonito, J D.]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAS141_03721 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314267 Sulfitobacter sp. NAS-14.1])</td></tr>
-	[[Category: Chowdhury, S.]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nx1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nx1 RCSB], [http://www.ebi.ac.uk/pdbsum/4nx1 PDBsum]</span></td></tr>
-	[[Category: EFI, Enzyme Function Initiative.]]	+	</table>
-	[[Category: Evans, B.]]	+	__TOC__
-	[[Category: Gerlt, J A.]]	+	</StructureSection>
-	[[Category: Glenn, A Scott.]]	+	[[Category: Sulfitobacter sp. nas-14 1]]
-	[[Category: Hillerich, B.]]	+	[[Category: Almo, S C]]
-	[[Category: Imker, H J.]]	+	[[Category: Attonito, J D]]
-	[[Category: Love, J.]]	+	[[Category: Chowdhury, S]]
-	[[Category: Morisco, L L.]]	+	[[Category: EFI, Enzyme Function Initiative]]
-	[[Category: Obaidi, N F.Al.]]	+	[[Category: Evans, B]]
-	[[Category: Seidel, R D.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Sojitra, S.]]	+	[[Category: Glenn, A Scott]]
-	[[Category: Stead, M.]]	+	[[Category: Hillerich, B]]
-	[[Category: Vetting, M W.]]	+	[[Category: Imker, H J]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Love, J]]
		+	[[Category: Morisco, L L]]
		+	[[Category: Obaidi, N F.Al]]
		+	[[Category: Seidel, R D]]
		+	[[Category: Sojitra, S]]
		+	[[Category: Stead, M]]
		+	[[Category: Vetting, M W]]
		+	[[Category: Wasserman, S R]]
	[[Category: Efi]]		[[Category: Efi]]
	[[Category: Enzyme function initiative]]		[[Category: Enzyme function initiative]]

OCA at 07:05, 22 January 2014

OCA — Wed, 22 Jan 2014 07:05:45 GMT

←Older revision		Revision as of 07:05, 22 January 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nx1\| PDB=4nx1 \| SCENE= }}
		+	===Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate===

-	~~The entry~~ 4nx1 is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4nx1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NX1 OCA].
-	~~Authors~~: ~~Vetting, M~~.W.~~, Al Obaidi, N~~.F.~~, Morisco, L.L., Wasserman~~, S.~~R., Sojitra, S., Stead, M.,~~ Attonito, J.D.~~, Scott Glenn, A.,~~ Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., ~~Imker, H.J~~., ~~Gerlt, J~~.A.~~, Almo~~, S.~~C.,~~ Enzyme ~~Function Initiative (EFI)~~	+	[[Category: Almo, S C.]]
-		+	[[Category: Attonito, J D.]]
-	~~Description~~: ~~Crystal structure of a trap~~ periplasmic solute binding ~~protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate~~	+	[[Category: Chowdhury, S.]]
		+	[[Category: EFI, Enzyme Function Initiative.]]
		+	[[Category: Evans, B.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Glenn, A Scott.]]
		+	[[Category: Hillerich, B.]]
		+	[[Category: Imker, H J.]]
		+	[[Category: Love, J.]]
		+	[[Category: Morisco, L L.]]
		+	[[Category: Obaidi, N F.Al.]]
		+	[[Category: Seidel, R D.]]
		+	[[Category: Sojitra, S.]]
		+	[[Category: Stead, M.]]
		+	[[Category: Vetting, M W.]]
		+	[[Category: Wasserman, S R.]]
		+	[[Category: Efi]]
		+	[[Category: Enzyme function initiative]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transport protein]]
		+	[[Category: Trap periplasmic solute binding family]]

OCA at 09:27, 25 December 2013

OCA — Wed, 25 Dec 2013 09:27:28 GMT

←Older revision		Revision as of 09:27, 25 December 2013
Line 5:		Line 5:
	Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)		Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

-	Description: ~~CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER~~ sp. ~~NAS~~-14.1, ~~TARGET~~ EFI-510292, ~~WITH BOUND~~ alpha-D-~~TALURONATE~~	+	Description: Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate

OCA: Protected "4nx1" [edit=sysop:move=sysop]

OCA — Wed, 18 Dec 2013 09:25:02 GMT

Protected "4nx1" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:25, 18 December 2013

OCA: New page: '''Unreleased structure''' The entry 4nx1 is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

OCA — Wed, 18 Dec 2013 09:25:00 GMT

New page: '''Unreleased structure''' The entry 4nx1 is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

New page

'''Unreleased structure'''

The entry 4nx1 is ON HOLD

Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Description: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1, TARGET EFI-510292, WITH BOUND alpha-D-TALURONATE